Function Repository Resource:

BioSequenceMoleculePlot

Source Notebook

Visualize a biomolecular sequence with highlighted residues

Contributed by: Jan Mangaldan

ResourceFunction["BioSequenceMoleculePlot"][bioseq]

creates a two-dimensional structure diagram of the biomolecular sequence bioseq, where all residues are highlighted.

Details and Options

If bioseq is a BioSequence of type "Peptide" or "CircularPeptide", individual amino acids comprising the peptide are highlighted.
If bioseq is a BioSequence of type "DNA", "RNA", "CircularDNA" or "CircularRNA", individual nucleobases are highlighted.
Hybrid strands and sequence collections are supported.
ResourceFunction["BioSequenceMoleculePlot"] returns a Graphics expression.
ResourceFunction["BioSequenceMoleculePlot"] has the same options as MoleculePlot, with the following additions:
"Highlighting"Automatichow to highlight the given BioSequence
With "Highlighting""ResidueSugar", the phosphate groups and sugars in DNA and RNA sequences are highlighted separately. With "Highlighting""ResidueBackbone", the phosphate groups and sugars are highlighted with a single color.

Examples

Basic Examples (1) 

Visualize the structure of the "beefy meaty peptide":

In[1]:=
ResourceFunction["BioSequenceMoleculePlot"][
 BioSequence["Peptide", "KGDEESLA"]]
Out[1]=

Scope (2) 

Visualize the structure of the circular peptide evolidine:

In[2]:=
ResourceFunction["BioSequenceMoleculePlot"][
 BioSequence["CircularPeptide", "SFLPVNL"]]
Out[2]=

Compare an RNA and a circular RNA sequence:

In[3]:=
{ResourceFunction["BioSequenceMoleculePlot"][
   BioSequence["RNA", "AUCGCCGUG"]], ResourceFunction["BioSequenceMoleculePlot"][
   BioSequence["CircularRNA", "AUCGCCGUG"]]} // GraphicsRow
Out[3]=

Options (2) 

Highlighting (2) 

Highlight the sugars and phosphate groups together in a DNA-RNA hybrid strand:

In[4]:=
ResourceFunction["BioSequenceMoleculePlot"][
 BioSequence[
  "HybridStrand", {BioSequence["DNA", "TGC"], BioSequence["RNA", "GUA"]}], "Highlighting" -> "ResidueBackbone"]
Out[4]=

Highlight the sugars and phosphate groups separately:

In[5]:=
ResourceFunction["BioSequenceMoleculePlot"][
 BioSequence[
  "HybridStrand", {BioSequence["DNA", "TGC"], BioSequence["RNA", "GUA"]}], "Highlighting" -> "ResidueSugar"]
Out[5]=

Neat Examples (1) 

Highlight the amino acid residues in human insulin:

In[6]:=
ResourceFunction["BioSequenceMoleculePlot"][
BioSequence[{
BioSequence["Peptide", "FVNQHLCGSHLVEALYLVCGERGFFYTPKT", {}], 
BioSequence["Peptide", "GIVEQCCTSICSLYQLENYCN", {}]}, {
Bond[{{2, 1, 6}, {2, 1, 11}}, "DisulfideBridges"], 
Bond[{{2, 1, 7}, {1, 1, 7}}, "DisulfideBridges"], 
Bond[{{2, 1, 20}, {1, 1, 19}}, "DisulfideBridges"]}]]
Out[6]=

Version History

  • 1.0.0 – 07 February 2022

Related Resources

License Information